/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.utils.clip;

/**
 * Author: wbc
 */
public enum ClippingRepresentation {
    /** Clipped bases are changed to Ns */
    WRITE_NS,

    /** Clipped bases are changed to have Q0 quality score */
    WRITE_Q0S,

    /** Clipped bases are change to have both an N base and a Q0 quality score */
    WRITE_NS_Q0S,

    /**
     * Change the read's cigar string to soft clip (S, see sam-spec) away the bases.
     * Note that this can only be applied to cases where the clipped bases occur
     * at the start or end of a read.
     */
    SOFTCLIP_BASES,

    /**
     * WARNING: THIS OPTION IS STILL UNDER DEVELOPMENT AND IS NOT SUPPORTED.
     *
     * Change the read's cigar string to hard clip (H, see sam-spec) away the bases.
     * Hard clipping, unlike soft clipping, actually removes bases from the read,
     * reducing the resulting file's size but introducing an irrevesible (i.e.,
     * lossy) operation.  Note that this can only be applied to cases where the clipped
     * bases occur at the start or end of a read.
     */
    HARDCLIP_BASES,

    /**
     * Turn all soft-clipped bases into matches
     */
    REVERT_SOFTCLIPPED_BASES,
}
